APOPTOSIS / cytochrome / electron transport / Apaf-1 / Heme / mitochondia
Function / homology
Function and homology information
Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / cellular respiration / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / cellular respiration / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / Detoxification of Reactive Oxygen Species / Pyroptosis / respirasome / intrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / Cytoprotection by HMOX1 / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / metal ion binding / nucleus / cytosol Similarity search - Function
Monochromator: Osmic VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54 Å / Relative weight: 1
Reflection
Resolution: 1.9→19.79 Å / Num. all: 32147 / Num. obs: 30928 / % possible obs: 96.2 % / Redundancy: 3.13 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.7
Reflection shell
Resolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3172 / % possible all: 93.6
-
Processing
Software
Name
Version
Classification
CrystalClear
datacollection
PHASER
phasing
REFMAC
5.5.0109
refinement
d*TREK
datareduction
d*TREK
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.79 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.707 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24717
1566
5.1 %
RANDOM
Rwork
0.17215
-
-
-
all
0.176
30733
-
-
obs
0.17598
29167
95.98 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 26.594 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.75 Å2
0 Å2
-0.2 Å2
2-
-
-0.55 Å2
0 Å2
3-
-
-
-0.2 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→19.79 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3268
0
172
381
3821
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.023
0.022
3532
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.861
2.127
4772
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.115
5
412
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.084
25
128
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.896
15
680
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
32.646
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.126
0.2
464
X-RAY DIFFRACTION
r_gen_planes_refined
0.012
0.021
2572
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.868
1.5
2044
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
3.223
2
3268
X-RAY DIFFRACTION
r_scbond_it
4.44
3
1488
X-RAY DIFFRACTION
r_scangle_it
6.619
4.5
1504
X-RAY DIFFRACTION
r_rigid_bond_restr
2.597
3
3532
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.349
114
-
Rwork
0.25
2071
-
obs
-
-
93.34 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.0228
-0.059
-0.0369
0.1811
0.1215
0.0858
-0.0238
-0.0047
0.0092
-0.0036
0.0263
0.006
-0.0257
0.0106
-0.0025
0.1465
0.0072
0.0092
0.1881
0.0006
0.1882
-7.6708
-31.8982
2.5828
2
0.0615
-0.0222
-0.0387
0.0085
0.014
0.0247
0
0.0105
-0.0056
-0.0002
-0.003
-0.0077
0.007
-0.0042
0.0029
0.1511
0.0005
0.0052
0.1904
0.0008
0.1811
-13.1982
-16.4498
2.0934
3
0.2293
-0.1024
-0.0538
0.1598
0.4119
1.3485
-0.0112
0.0132
0.0147
0.0218
0.0032
-0.0061
0.0108
0.0246
0.008
0.1377
0.002
0.0209
0.1855
-0.0084
0.1564
-15.3547
-29.9148
1.8864
4
0.0093
0.0374
-0.0038
0.1568
-0.013
0.0039
-0.0103
0.0033
-0.0065
0.0052
0.0159
-0.0287
0.0166
-0.0142
-0.0055
0.1406
-0.0065
0.0067
0.1936
-0.0029
0.1938
-7.3762
19.1516
15.2203
5
0.0336
-0.0002
0.0011
0
0
0.0001
0.0018
-0.0117
-0.0046
0.0016
-0.0022
-0.0013
-0.0016
-0.0019
0.0004
0.1539
-0.0009
0.0079
0.1916
0.0003
0.1824
-12.9903
4.2766
16.172
6
0.2208
0.1383
0.1354
0.0876
0.086
0.0854
0.0201
-0.0051
-0.0199
0.0118
0.0073
-0.0208
0.0218
0.0063
-0.0275
0.1487
0.0009
0.0057
0.1901
-0.0022
0.1781
-15.6608
17.0191
14.0789
7
0.3195
-0.007
-0.0224
0.0004
0.0003
0.0019
-0.0067
0.0071
-0.0119
-0.0033
0.0054
0
0.0075
-0.0015
0.0013
0.1494
0.0014
0.0078
0.1915
-0.0011
0.1835
-33.9287
-19.8867
24.6838
8
0.0001
0
0.0001
0
0
0.0002
-0.0028
0.0023
0.0009
-0.0009
-0.0013
-0.0026
-0.0031
0.0006
0.0041
0.1535
0.0002
0.0064
0.1916
0
0.1822
-36.1875
-23.3163
8.9344
9
4.3135
-2.9334
2.5665
7.3404
-4.3061
2.7546
-0.0111
-0.184
0.0682
0.6785
-0.0295
-0.0017
-0.3346
-0.0369
0.0406
0.0844
-0.0021
-0.0039
0.1564
-0.0198
0.062
-35.6249
-7.2115
18.891
10
0.2217
-0.031
0.1984
0.0056
-0.0289
0.1792
0.0085
0.0016
0.0069
-0.0158
-0.0034
-0.0012
0.0241
-0.0053
-0.0051
0.1571
0.0021
0.0075
0.1686
0.0043
0.1875
-27.6385
-19.6015
18.7603
11
0.0032
0.0077
0.0006
0.0778
-0.0225
0.0111
-0.0142
0.0027
0.0171
-0.0126
0.005
0.0035
-0.0174
0.0093
0.0092
0.1521
-0.0006
0.0054
0.1922
0.0032
0.1792
-34.076
6.9444
-7.0727
12
0.0802
-0.0507
-0.0314
0.0321
0.0199
0.0123
-0.0024
0.0022
-0.0069
-0.0013
0.0015
0.0046
0.0008
-0.0004
0.0008
0.1536
-0.002
0.0032
0.1887
0
0.1794
-36.107
10.7623
8.7604
13
3.02
-0.1373
-0.0398
0.0277
-0.1942
1.9037
-0.0584
-0.1204
-0.184
0.0177
-0.0053
-0.005
-0.037
0.0585
0.0636
0.148
-0.0061
0.0108
0.1683
-0.0058
0.1594
-35.3634
-5.0839
-1.6473
14
0.5124
0.3318
-0.2946
0.2673
-0.1422
0.2176
0.0109
0.0262
-0.0053
0.0341
0.0078
-0.0103
-0.0049
0.0036
-0.0187
0.1536
-0.0034
0
0.1808
-0.0029
0.1826
-27.6672
6.6736
-0.8958
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 16
2
X-RAY DIFFRACTION
2
A
17 - 85
3
X-RAY DIFFRACTION
3
A
86 - 104
4
X-RAY DIFFRACTION
4
B
1 - 16
5
X-RAY DIFFRACTION
5
B
17 - 87
6
X-RAY DIFFRACTION
6
B
88 - 104
7
X-RAY DIFFRACTION
7
C
1 - 16
8
X-RAY DIFFRACTION
8
C
17 - 84
9
X-RAY DIFFRACTION
9
C
85 - 89
10
X-RAY DIFFRACTION
10
C
90 - 104
11
X-RAY DIFFRACTION
11
D
1 - 16
12
X-RAY DIFFRACTION
12
D
17 - 84
13
X-RAY DIFFRACTION
13
D
85 - 89
14
X-RAY DIFFRACTION
14
D
90 - 104
+
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